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  • Leah here from leah4sci.com/mcat and in this video we'll start the introduction to Amino

  • Acids as you have to know them for the mcat and potentially your biochemistry class. This

  • video we'll look at the basics and the remainder of this series will break it down step by

  • step to make sure that you understand every single aspect. The first question to ask yourself

  • is What is an Amino Acid? Every Amino Acid has a central carbon called the alpha carbon.

  • Then we have the amino portion which is an amine group NH2 and an acid portion which

  • is a carboxylic acid. There is also a hydrogen atom and a variable group called the R-group

  • which is the rest of the molecule and this will change from amino acid to amino acid.

  • We said the central carbon is called the Alpha Carbon and this goes back to something you

  • learned in Organic Chemistry. When you had a carbon chain with a carbonyl, that carbonyl

  • was the starting carbon, like the ground zero where you start counting. The first carbon

  • attached to that was called the Alpha carbon. The second carbon attached was the beta carbon,

  • the third is the gamma carbon, and then the delta and so on, and so on. For the amino

  • acid, if the carboxylic acid has a carbonyl at zero, the central carbon attached to the

  • carbonyl is the first one and therefore the alpha carbon. This form of drawing a neutral

  • amino acid is technically incorrect because it can't exist like this in nature. The amino

  • acid naturally exists as having two ions in the backbone that cancels each other out.

  • This is called the dipolar ion or the zwitterion and this can change depending on the specific

  • ph, something we'll look at in this zwitterion tutorial. For now, just realize that if we

  • take away the hydrogen on the carboxyl, we get an Oxygen with three lone pairs and a

  • negative charge. And if we add a hydrogen to the amino we get four bonds to Nitrogen,

  • we took away its lone pair and we get a positive charge.

  • We'll show the amino acid as AA for short. And notice in the backbone we have 4 common

  • atoms. We have carbon, oxygen, nitrogen, and hydrogen. Two of the R-groups also have sulfur

  • and this is important for being able to distinguish between amino acids and nucleotides which

  • is another very important molecule in a living system. Nucleotides which make up DNA and

  • RNA also have carbon, oxygen, nitrogen, and hydrogen but they have a phosphorous in their

  • backbone and they don't have sulfur so that's the qa to distinguish which type of molecule

  • it came from. And why are amino acids so important? They are the monomers, the single unit that

  • make up a very important structure key to the survival of a cell and that is proteins.

  • Proteins forms so many important critical structures of the cell, from holding it together

  • like the cytoskeleton, enzymes that catalyze reactions, structural components for example

  • in the cell membranes or holding proteins, dna, and different things together, transport

  • in signalling so we have proteins acting as carrier molecules, peptide hormones which

  • are made up of Amino Acids and we can even use it for energy on the cell if we need to.

  • And these are just some examples.

  • Amino acids are the building blocks of proteins. And if you take the twenty most common amino

  • acids, and you change the sequence in which they're attached, and the link of the chain

  • you get an infinite number of possibilities of different types of proteins that can be

  • formed. There are twenty common amino acids that you need to know for the MCAT. Understand

  • that there can be more, through modification or rare ones, but the twenty common ones are

  • the ones you need to memorize. These can be broken down into essential amino acids, meaning

  • the body can't synthesize these amino acids so you have to get it from your diet. And

  • then the non-essential amino acids which your body can synthesize using the essential amino

  • acids as the starting point. You don't have to memorize this but the 9 essential amino

  • acids are histidine, leucine, isoleucine, lysine, methionine, phenylalanine, threonine,

  • tryptophan, and valine.

  • The non-essential include the conditionally essential but we'll just classify them as

  • non-essential in general which means that the body can make them depending on the circumstances.

  • That includes alanine, asparagine, aspartic acid, and arginine, glutamic acid, glutamine,

  • glycine, proline, serine, tyrosine, and cysteine. What sets these amino acids apart? It's the

  • R-group. The r-group is a variable group and this is what changes from amino acid to amino

  • acid. This group gives the amino acid its special characteristics, determines how it

  • interacts with other amino acids and ultimately determines how it interacts with this environment

  • and all the molecules around it. The amino acids will be classified based on the chemistry

  • of that R-group. We can simply separate them into the hydrophobic and hydrophilic groups.

  • Instead of memorizing why an amino acid falls into a certain category, I want you to understand

  • what about the chemistry of the R-group makes it fall into that category. That way when

  • you look at the side chain, you'll be able to look at it and understand what's going

  • on. If you break this word down, we have hydrophobic means fearing and philic means loving.

  • Water is a very common molecule. Most of the world is made up of water and even most of

  • your body is water. Water has one oxygen atom and two hydrogen atoms. Oxygen is highly electronegative,

  • that means even though it's bound to hydrogen with a covalent bond, a sharing bond, Oxygen

  • is greedy and it tries to pull on the electrons from the bond towards itself. In pulling down

  • those electrons we have a pulling or polar bond and this concentrates the negativity

  • of the bond around the oxygen taking it away from hydrogen. That extra negativity around

  • the oxygen makes it partially negative, and hydrogen having its positive nucleus exposed

  • is now partially positive. That gives the oxygen portion of water a partial negative

  • charge, the hydrogen portion, a partial positive charge, and this polarity allows it to interact

  • with other molecules, like water molecules or amino acid side chains.

  • When you look at a side chain, ask yourself, does it want to interact with water? Does

  • it have a charge or partial charge that can associate with the partial negative oxygen

  • or partial positive hydrogen? Or is it completely hydrophobic meaning it fears water because

  • it has no way to interact with it. Hydrophobic is non-polar, there is no polarity to interact

  • with water and hydrophilic side chains will be polar, meaning they have partial charges

  • or fully charged like your acidic and basic side chains. The hydrophobic side chains can

  • be broken up into two categories, the Aliphatic, and Aromatic side chains. These are terms

  • you should recognize from Organic chemistry. Aliphatic is linear, non-cyclical. It doesn't

  • have aromaticity so think of these as your linear or non-aromatic side chains. Aromatic

  • side-chains have aromatic groups within them. For example, benzene or even heterocyclic

  • aromatic compounds. See the link below if you need a review on aromaticity.

  • Hydrophilic side chains can also be broken down. We said that hydrophilic side chains

  • can be polar. That means partial charges but not full charges. And if we don't have a full

  • charge, then the side chain is neutral. What you're looking for in these side chains are

  • oxygen and nitrogen atoms, but without a protonation-deprotonation going on. For the charged side chain, we're

  • going to see acidic and basic components. The charged side chains can get a charge by

  • donating or accepting a proton. Donating a proton acid or accepting a proton base. And

  • yes, we'll break them all down in the upcoming videos.

  • Another thing to keep in mind is that amino acids have chirality or stereochemistry. In

  • Organic Chemistry you learn this as R&S, but in biochemistry we'll use the configuration

  • of D&L. The amino acid chirality video, we'll break it down and show you how to find the

  • chirality but for now keep this in mind, Eukaryotic organisms like the L form of amino acids and

  • they don't like the D form of amino acids. If you're asking, does D&L convert to R&S?

  • the answer is, it can be both. R&S does not specifically tell me D&L and I'll show you

  • how to recognize this in the amino acid chirality video.

  • And finally, in understanding amino acids as an essential component of protein, it's

  • critical to understand how they react. Later in this series, we'll look at three important

  • amino acid reactions. When amino acids are brought together, they form a peptide bond

  • and you can think of this as dehydration synthesis because you're synthesizing the bond, you're

  • bringing the two amino acids together and in the process taking out a molecule of H2O.

  • If connecting amino acids takes out the water molecule, then you can imagine that to break

  • apart a peptide bond into the separate acids, you have to put the water back. And this is

  • called the hydrolysis reaction. Which comes from the word, hydro, adding the water back

  • in, and lysis to break. Another critical reaction is Sulfur linkage creating disulfide bridges,

  • and this is the only covalent bond that forms between amino acid side chains to strengthen

  • that three dimensional tertiary or Quaternary protein structure.

  • Now that you have an idea of what you need to know, let's break it down step by step.

  • Make sure you download the amino acid cheat sheet so you can follow along as you watch

  • this entire series and then try the amino acid practice quiz. You can find all of these

  • on my website leah4sci.com/AminoAcids.

Leah here from leah4sci.com/mcat and in this video we'll start the introduction to Amino

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